Paul Pavlidis

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 10

Top Topics

Functional Analysis

High Throughput

Transcriptional Regulatory

Top Venues

PLoS Comput. Biol.

Database J. Biol. Databases Curation

Frontiers Neuroinformatics

Publications

Rachel J. Harding, Patrick Bermudez, Alexander Bernier, Michael Beauvais, Pierre Bellec, Sean L. Hill, Agah Karakuzu, Bartha M. Knoppers, Paul Pavlidis, Jean-Baptiste Poline, Jane Roskams, Nikola Stikov, Jessica Stone, Stephen C. Strother, CONP Consortium, Alan C. Evans
The Canadian Open Neuroscience Platform - An open science framework for the neuroscience community. PLoS Comput. Biol. 19 (7) (2023)
Eric Ching-Pan Chu, Alexander Morin, Tak Hou Calvin Chang, Tue Nguyen, Yi-Cheng Tsai, Aman Sharma, Chao Chun Liu, Paul Pavlidis
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PLoS Comput. Biol. 17 (10) (2021)
Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, Burak Ogan Mancarci, Jordan Sicherman, Matthew Jacobson, Justin Leong, Patrick Tan, Paul Pavlidis
Curation of over 10 000 transcriptomic studies to enable data reuse. Database J. Biol. Databases Curation 2021 (2021)
Marjan Farahbod, Paul Pavlidis
Differential coexpression in human tissues and the confounding effect of mean expression levels. Bioinform. 35 (1) (2019)
Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes. PLoS Comput. Biol. 15 (6) (2019)
Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis
Transcriptomic correlates of neuron electrophysiological diversity. PLoS Comput. Biol. 13 (10) (2017)
Nikolaus Fortelny, Christopher M. Overall, Paul Pavlidis, Gabriela V. Cohen Freue
Can we predict protein from mRNA levels? Nat. 547 (7663) (2017)
Sara Ballouz, Melanie Weber, Paul Pavlidis, Jesse A. Gillis
EGAD: ultra-fast functional analysis of gene networks. Bioinform. 33 (4) (2017)
Andra Waagmeester, Egon L. Willighagen, Núria Queralt-Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E. Putman, Julia Turner, Lynn M. Schriml, Paul Pavlidis, Andrew I. Su, Benjamin M. Good
Linking Wikidata to the Rest of the Semantic Web. SWAT4LS (2016)
Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim E. Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su
Wikidata as a semantic framework for the Gene Wiki initiative. Database J. Biol. Databases Curation 2016 (2016)
Nikolaus Fortelny, Sharon Yang, Paul Pavlidis, Philipp F. Lange, Christopher M. Overall
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Res. 43 (Database-Issue) (2015)
Leon French, Po Liu, Olivia Marais, Tianna Koreman, Lucia Tseng, Artemis Lai, Paul Pavlidis
Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application. Frontiers Neuroinformatics 9 (2014)
Jesse A. Gillis, Paul Pavlidis
Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinform. 29 (4) (2013)
Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355-1363]. NeuroImage 72 (2013)
Jesse A. Gillis, Paul Pavlidis
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinform. 14 (S-3) (2013)
Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity. PLoS Comput. Biol. 8 (3) (2012)
Paul Pavlidis, Jesse A. Gillis
Progress and challenges in the computational prediction of gene function using networks. F1000Research 1 (2012)
Jesse A. Gillis, Paul Pavlidis
"Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. PLoS Comput. Biol. 8 (3) (2012)
Leon French, Suzanne Lane, Lydia Xu, Celia Siu, Cathy Kwok, Yiqi Chen, Claudia Krebs, Paul Pavlidis
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. Bioinform. 28 (22) (2012)
Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch
Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing. NeuroImage 61 (4) (2012)
Anton Zoubarev, Kelsey M. Hamer, Kiran Keshav, E. Luke McCarthy, Joseph Roy C. Santos, Thea Van Rossum, Cameron McDonald, Adam Hall, Xiang Wan, Raymond Lim, Jesse A. Gillis, Paul Pavlidis
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinform. 28 (17) (2012)
Jesse A. Gillis, Paul Pavlidis
The role of indirect connections in gene networks in predicting function. Bioinform. 27 (13) (2011)
Leon French, Paul Pavlidis
Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain. PLoS Comput. Biol. 7 (1) (2011)
Leon French, Powell Patrick Cheng Tan, Paul Pavlidis
Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. Frontiers Neuroinformatics 5 (2011)
Leon French, Suzanne Lane, Tamryn Law, Lydia Xu, Paul Pavlidis
Application and evaluation of automated semantic annotation of gene expression experiments. Bioinform. 25 (12) (2009)
Leon French, Suzanne Lane, Lydia Xu, Paul Pavlidis
Automated recognition of brain region mentions in neuroscience literature. Frontiers Neuroinformatics 3 (2009)
Jesse A. Gillis, Paul Pavlidis
A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinform. 10 (2009)
Meeta Mistry, Paul Pavlidis
Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinform. 9 (2008)
Xiang Wan, Paul Pavlidis
Sharing and Reusing Gene Expression Profiling Data in Neuroscience. Neuroinformatics 5 (3) (2007)
Leon French, Paul Pavlidis
Informatics in neuroscience. Briefings Bioinform. 8 (6) (2007)
Homin K. Lee, William Braynen, Kiran Keshav, Paul Pavlidis
ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinform. 6 (2005)
Paul Pavlidis
Book Review. J. Biomed. Informatics 37 (1) (2004)
Paul Pavlidis, Ilan Wapinski, William Stafford Noble
Support vector machine classification on the web. Bioinform. 20 (4) (2004)
Paul Pavlidis, Qinghong Li, William Stafford Noble
The effect of replication on gene expression microarray experiments. Bioinform. 19 (13) (2003)
Paul Pavlidis, William Stafford Noble
Matrix2png: a utility for visualizing matrix data. Bioinform. 19 (2) (2003)
Hanga C. Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P. Ellis, J. John Mann, Etienne Sibille, Victoria Arango
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinform. 4 (2003)
Paul Pavlidis, Darrin P. Lewis, William Stafford Noble
Exploring Gene Expression Data with Class Scores. Pacific Symposium on Biocomputing (2002)
Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble
Learning Gene Functional Classifications from Multiple Data Types. J. Comput. Biol. 9 (2) (2002)
Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy
Gene functional classification from heterogeneous data. RECOMB (2001)
Paul Pavlidis, Terrence S. Furey, M. Liberto, David Haussler, William Noble Grundy
Promoter Region-Based Classification of Genes. Pacific Symposium on Biocomputing (2001)
Paul Pavlidis, Christopher Tang, William Stafford Noble
Classification of genes using probabilistic models of microarray expression profiles. BIOKDD (2001)